Simulate an alignmentΒΆ

Section author: Gavin Huttley

How to simulate an alignment. For this example we just create a simple model using a four taxon tree with very different branch lengths, a Felsenstein model with very different nucleotide frequencies and a long alignment.

See the other examples for how to define other substitution models.

>>> import sys
>>> from cogent import LoadTree
>>> from cogent.evolve import substitution_model

Specify the 4 taxon tree,

>>> t = LoadTree(treestring='(a:0.4,b:0.3,(c:0.15,d:0.2)edge.0:0.1);')

Define our Felsenstein 1981 substitution model.

>>> sm = substitution_model.Nucleotide(motif_probs = {'A': 0.5, 'C': 0.2,
... 'G': 0.2, 'T': 0.1}, model_gaps=False)
>>> lf = sm.makeLikelihoodFunction(t)
>>> lf.setConstantLengths()
>>> lf.setName('F81 model')
>>> print lf
F81 model
==========================
  edge    parent    length
--------------------------
     a      root    0.4000
     b      root    0.3000
     c    edge.0    0.1500
     d    edge.0    0.2000
edge.0      root    0.1000
--------------------------
===============
motif    mprobs
---------------
    T    0.1000
    C    0.2000
    A    0.5000
    G    0.2000
---------------

We’ll now create a simulated alignment of length 1000 nucleotides.

>>> simulated = lf.simulateAlignment(sequence_length=1000)

The result is a normal Cogent alignment object, which can be used in the same way as any other alignment object.